Contents of this Article

The Open Vector Editor (OVE) is a user-friendly open-source tool to view, design, edit, and annotate plasmids and their sequences. This allows you to see your sequence properties and to work with them; this article focuses on the available Tools of the OVE (to get to know more about the View of a sequence, go to this article instead).

On the different tabs, you can see the general sequence information, features list, DNA parts list, primers, translations, cut sites (filtered by enzyme type), and ORFs. On some tabs, you have the option to create new ones, remove duplicates, and change the visibility filter. On the last tab, you can see your sequence(s) in different formats: GenBank, FASTA, and JSON.

As you can see on the primers tab of the OVE, it is possible to simulate a PCR from it:

Notice that this option shows the available primers, which you need to have before running a PCR simulation. Next, let's see how to prepare everything before simulating a PCR.

First, select your complete sequence, or the portion that you want to amplify with your PCR. Then, right-click on it and select Create > Create PCR primers for this region.

This will open a window where you can indicate the part name (from the already-existing parts, or by creating a new one). Also, you can indicate your preferences on your primers characteristics.

After hitting "Ok" you will see a pop-up window indicating that you have successfully created a new design, where you can click on "Submit for Assembly" to create your primers. There are two ways to see your Assembly Report: from the notifications tab or on the DNA Assembly Reports library from the Molecular Biology Toolkit.

On the report, locate the "Assembly Oligos" section.

Now, click on "Save to Oligo Library".